640x480 is pretty high for a pixel art game. If you plan to go that high wouldn't it be better to just use regular 2D painting techniques?
Here's an interesting article on pixel art if you haven't read it:
gamedeveloper.com/game-platforms
And an exerpt:
nfortunately, a facet of this problem extends even to well-planned, well-intentioned projects. It's a quadratic problem; that is, doubling the resolution of your project actually quadruples the size of the art assets. After all, you can fit four 64x64 images into a 128x128 image. In many 2D mediums that just means using a bigger brush, no big deal, but in pixel art the ramifications are pretty serious. When you are painting your lines and details and anti-aliasing pixel by precious pixel you have 4 times as many elements to manipulate with tender, obsessive care.